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  • akkiMay 19, 2009 1:31 AM PDT   
    Length of a DNA sequence
    Is there a limit on the length of a DNA sequence in the database file?

    Clay Breshears (Intel)May 21, 2009 2:23 PM PDT
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    		 #1
    Re: Length of a DNA sequence
    Quoting - akki
    Is there a limit on the length of a DNA sequence in the database file?

    Well, the Amoeba dubia has 670 billion base pairs, but that seems a bit excessive.  Humans have around 3.2 billion base pairs.  Again, probably too big for our purposes.

    Let's put a limit of 1 million (10^6) base pairs per sequence.  That would mean 12501 lines for one sequence (1 descriptor line and 12500 lines of sequence).

    --clay

    akkiMay 22, 2009 1:02 AM PDT
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    		 #2 Reply To #1
    Re: Length of a DNA sequence

    Well, the Amoeba dubia has 670 billion base pairs, but that seems a bit excessive.  Humans have around 3.2 billion base pairs.  Again, probably too big for our purposes.

    Let's put a limit of 1 million (10^6) base pairs per sequence.  That would mean 12501 lines for one sequence (1 descriptor line and 12500 lines of sequence).

    --clay

    Thanks clay.

    My math is somewhat rusty so, please correct me if I miscalculated. But, with the 231 - 1 (> 2 * 109) limit specified for the number of sequences in another post (http://software.intel.com/en-us/forums/showthread.php?t=65703), and 1 million byte-long sequences (106), do I really need to make provisions for 2 * 1015 (~ 2 Petabytes) of storage for each file?! :O

    What I'm really wondering is, does this mean that I cannot read everything (or at least one of the files) into memory at the beginning?


    邓辉May 24, 2009 9:40 AM PDT
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    		 #3 Reply To #2
    Re: Length of a DNA sequence
    Quoting - akki

    Thanks clay.

    My math is somewhat rusty so, please correct me if I miscalculated. But, with the 231 - 1 (> 2 * 109) limit specified for the number of sequences in another post (http://software.intel.com/en-us/forums/showthread.php?t=65703), and 1 million byte-long sequences (106), do I really need to make provisions for 2 * 1015 (~ 2 Petabytes) of storage for each file?! :O

    What I'm really wondering is, does this mean that I cannot read everything (or at least one of the files) into memory at the beginning?
    Hope that the proportion of documents to read and write will be accounted for less


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    lixianyuMay 25, 2009 8:46 AM PDT
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    		 #4 Reply To #2
    Re: Length of a DNA sequence
    Quoting - akki

    Thanks clay.

    My math is somewhat rusty so, please correct me if I miscalculated. But, with the 231 - 1 (> 2 * 109) limit specified for the number of sequences in another post (http://software.intel.com/en-us/forums/showthread.php?t=65703), and 1 million byte-long sequences (106), do I really need to make provisions for 2 * 1015 (~ 2 Petabytes) of storage for each file?! :O

    What I'm really wondering is, does this mean that I cannot read everything (or at least one of the files) into memory at the beginning?

    Yes, you're right! We can not read everything into memory at the beginning.

    Clay Breshears (Intel)May 27, 2009 10:29 AM PDT
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    		 #5 Reply To #2
    Re: Length of a DNA sequence
    Quoting - akki

    Thanks clay.

    My math is somewhat rusty so, please correct me if I miscalculated. But, with the 231 - 1 (> 2 * 109) limit specified for the number of sequences in another post (http://software.intel.com/en-us/forums/showthread.php?t=65703), and 1 million byte-long sequences (106), do I really need to make provisions for 2 * 1015 (~ 2 Petabytes) of storage for each file?! :O

    What I'm really wondering is, does this mean that I cannot read everything (or at least one of the files) into memory at the beginning?

    There doesn't seem to be anything wrong with your math.  In http://software.intel.com/en-us/forums/showthread.php?t=65734 I've stated the assumption that the raw database will fit into memory.

    --clay

    akkiMay 27, 2009 11:16 PM PDT
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    		 #6 Reply To #5
    Re: Length of a DNA sequence

    There doesn't seem to be anything wrong with your math.  In http://software.intel.com/en-us/forums/showthread.php?t=65734 I've stated the assumption that the raw database will fit into memory.

    --clay

    Alright. Thanks clay.


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